LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.52 3.52 3.52 Created orthogonal box = (0 -46.1679 0) to (32.6431 46.1679 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.07314 5.90474 4.97803 Created 694 atoms create_atoms CPU = 0.00037694 secs 694 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.07314 5.90474 4.97803 Created 694 atoms create_atoms CPU = 0.000260115 secs 694 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 8 22 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1368 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.916 | 5.916 | 5.916 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6034.6325 0 -6034.6325 4888.6732 58 0 -6065.8371 0 -6065.8371 -4168.4332 Loop time of 0.933739 on 1 procs for 58 steps with 1368 atoms 100.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6034.6324575 -6065.831359 -6065.83707202 Force two-norm initial, final = 25.2697 0.256517 Force max component initial, final = 5.36881 0.0222325 Final line search alpha, max atom move = 1 0.0222325 Iterations, force evaluations = 58 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.91408 | 0.91408 | 0.91408 | 0.0 | 97.89 Neigh | 0.0089619 | 0.0089619 | 0.0089619 | 0.0 | 0.96 Comm | 0.0065632 | 0.0065632 | 0.0065632 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004134 | | | 0.44 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9891 ave 9891 max 9891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 337920 ave 337920 max 337920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337920 Ave neighs/atom = 247.018 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.916 | 5.916 | 5.916 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -6065.8371 0 -6065.8371 -4168.4332 15004.432 59 0 -6065.843 0 -6065.843 -2836.7419 14993.128 Loop time of 0.028136 on 1 procs for 1 steps with 1368 atoms 106.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6065.83707202 -6065.83707202 -6065.84298018 Force two-norm initial, final = 21.3539 3.09067 Force max component initial, final = 18.5143 2.65085 Final line search alpha, max atom move = 5.40122e-05 0.000143178 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.027519 | 0.027519 | 0.027519 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016618 | 0.00016618 | 0.00016618 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004506 | | | 1.60 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900 ave 9900 max 9900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 339272 ave 339272 max 339272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 339272 Ave neighs/atom = 248.006 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.72488 ghost atom cutoff = 8.72488 binsize = 4.36244, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.054 | 6.054 | 6.054 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6065.843 0 -6065.843 -2836.7419 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1368 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900 ave 9900 max 9900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 339340 ave 339340 max 339340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 339340 Ave neighs/atom = 248.056 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 6.054 | 6.054 | 6.054 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -6065.843 -6065.843 32.634163 92.335775 4.9756496 -2836.7419 -2836.7419 283.19425 -8625.9651 -167.45495 2.2953156 925.09152 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1368 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.537e-07 | | |100.00 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9900 ave 9900 max 9900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 169670 ave 169670 max 169670 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 339340 ave 339340 max 339340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 339340 Ave neighs/atom = 248.056 Neighbor list builds = 0 Dangerous builds = 0 1368 -6034.99505876555 eV 2.29531557087915 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01